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- PDB-7zib: Crystal structure of dCK C4S-S74E mutant in complex with UDP and ... -

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Basic information

Entry
Database: PDB / ID: 7zib
TitleCrystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0635 inhibitor
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Inhibitor
Function / homology
Function and homology information


deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-J7I / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBen-Yaala, K. / Saez-Ayala, M. / Betzi, S. / Rebuffet, E. / Morelli, X.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARCSL220130606659 France
CitationJournal: Nat Commun / Year: 2023
Title: From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.
Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / ...Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / Voisset, E. / Montersino, C. / Castellano, R. / Collette, Y. / Asnafi, V. / Betzi, S. / Dubreuil, P. / Combes, S. / Morelli, X.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7384
Polymers32,7021
Non-polymers1,0363
Water1,26170
1
A: Deoxycytidine kinase
hetero molecules

A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4758
Polymers65,4032
Non-polymers2,0726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area3990 Å2
ΔGint-50 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.506, 68.506, 120.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Deoxycytidine kinase / dCK / Deoxyadenosine kinase / Deoxyguanosine kinase


Mass: 32701.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Escherichia coli (E. coli)
References: UniProt: P27707, deoxycytidine kinase, 2'-deoxyadenosine kinase, deoxyguanosine kinase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-J7I / 2-[2-[[5-[3-methoxy-4-(4-methylpiperazin-1-yl)sulfonyl-phenyl]-2-methyl-phenyl]-propyl-amino]-1,3-thiazol-4-yl]pyrimidine-4,6-diamine


Mass: 608.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N8O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1 M Sodium citrate, 67 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.93→45.21 Å / Num. obs: 22140 / % possible obs: 99.8 % / Redundancy: 9.386 % / Biso Wilson estimate: 45.345 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.082 / Χ2: 0.817 / Net I/σ(I): 16.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.93-2.059.2641.271.534930.5651.3599.7
2.05-2.1910.0280.6963.0432930.8510.735100
2.19-2.379.8460.3875.4130960.9460.409100
2.37-2.599.5560.238.8128410.9790.243100
2.59-2.98.7470.13114.4925940.9920.1499.8
2.9-3.349.790.07127.523200.9980.075100
3.34-4.099.2360.04940.719860.9990.05299.8
4.09-5.768.1830.04145.2515700.9980.04499.3
5.76-45.218.6670.03649.339470.9990.03898.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCG

4kcg


Resolution: 1.95→45.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.975 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1079 5 %RANDOM
Rwork0.1783 ---
obs0.1809 20501 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.17 Å2 / Biso mean: 42.052 Å2 / Biso min: 27.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.95→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 68 70 2046
Biso mean--50.91 42.98 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132032
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151866
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6622761
X-RAY DIFFRACTIONr_angle_other_deg1.3851.5854299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92623.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35615357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2671511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 76 -
Rwork0.286 1458 -
all-1534 -
obs--99.74 %

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